This study describes the transformation of molecular orientation which has a significant effect on the charge carrier mobility of organic thin film transistors. Theoretical analyses and molecular dynamics simulations are performed to uncover the mechanism of the orientation transformation of pentacene molecules on the amorphous SiO2 surface during the early stage of the physical vapor deposition process, where the initially grown lateral-oriented cluster will transfer to the normal-oriented one at a critical size n(c). The reorientation behavior is related to the competition between the molecule-molecule interactions and the molecule-substrate interactions. For small size clusters, the pentacene molecules are found to prefer to form a lateral-oriented cluster as driven by the molecule-substrate interactions, which can be increased by the existence of the sylanol groups on the amorphous SiO2 surface. Furthermore, when the molecular number n is greater than n(c), the normal orientation in the herringbone structure is gradually formed and becomes the stable configuration because the molecule-molecule interactions is dominant. (C) 2014 Elsevier B.V. All rights reserved,